Structure-based computational database screening, in vitro assay, and NMR assessment of compounds that target TAR RNA

There has been little prior effort to discover new drugs on the basis of a unique RNA structure. Binding of the viral transactivator Tat to the 5' bulge of the transactivation response (TAR) element is necessary for HIV-1 replication, so TAR RNA is a superb target. A computational approach was developed to screen a large chemical library for binding to a three-dimensional RNA structure. Scoring function development, flexible ligand docking, and limited target flexibility were essential. From the ranked list of compounds predicted to bind TAR, 43 were assayed for inhibition of the Tat-TAR interaction via electrophoretic mobility shift assays. Eleven compounds (between 0.1 and 1 muM) inhibited the Tat-TAR interaction, and some inhibited Tat transactivation in cells. NMR spectra verified specific binding to the 5' bulge and no interaction with other regions of TAR.